SHIELD must have access to all manner of experimental medical technology they could use to resuscitate a person who has died. Agents' employment contracts probably specify that in the event of their apparent death (whether brain death or merely the cessation of cardiac activity), SHIELD has the right to conduct experiments on the remains, including: the use of unconventional medical technology, zombification, nanotechnology, vampirism, induced lycanthropy, demonic possession, inhabitation by alien symbiote(s), transfer of consciousness into an android or cyborg body, meat puppetry, etc.

With options like those (and more) on the table, it would be easy to come up with a scenario that sees Agent Coulson returned from the great beyond physically intact and yet still somewhat the worse for wear. At the very least, the psychological ramifications of dying and being resurrected should be apparent in Phil's behavior.